This analysis can be used to identify quantitative trait locus (QTL) by displaying associations between markers and traits for trials within the T3 database.
Analysis Methods: The analysis includes genotype and phenotype trials where there were more than 50 germplasm lines in common.
1. Trial Analysis - GWAS with no fixed effects.
2. Breeding Program Analysis - GWAS on a set of related phenotype trials (different location and same year or same location different year). Principle Components that accounted for more than 5% of the relationship matrix variance were included as fixed effects in the analysis. Each phenotype trial (if more than one) was included as a fixed effect.
GWAS: The analysis use rrBLUP GWAS package (Endleman, Jeffery, "Ridge Regression and Other Kernels for Genomic Selection with R package rrBLUP", The Plant Genome Vol 4 no. 3). The settings are: MAF > 0.05, P3D = TRUE (equivalent to EMMAX). The q-value is an estimate of significance given p-values from multiple comparisons using a false discovery rate of 0.05.
The z-value = qnorm( 1.0 - ( pvalue / 2.0 ))

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Trait:

50 seed weightalpha amylasealpha-tocopherolalpha-tocotrienolamylose contentbarley colorbeta glucanbeta-glucanase thermostabilitybeta-tocopherolbeta-tocotrienolbreeders grain proteinbreeders plump grainBYDV rating (0-8)CRR Severitydelta-tocopheroldelta-tocotrienoldiastatic powerDONFHB IncidenceFHB reaction type (0-9)FHB Severityfree amino nitrogengamma-tocopherolgamma-tocopherol + beta-tocotrienolgamma-tocotrienolglossy sheathgrain hardnessgrain proteingrain weightgrain widthgrain yieldhead drop (0-9)heading dateheading date (Julian)head shatteringhull proportionkernels per spikekernel weightlemma and palea colorlipoxygenase activitylodgingmalt beta-glucanmalt extractnet blotch (1-10)non-dormant %phenolic compound contentplant heightplump grainpolyphenol oxidase activityproductive tillers per plantresidual beta-glucanasescald reaction type (0-9)Septoria seedling infection response (0-5)soluble protein/ total proteinspike anglespike lengthspikes per areaspot blotch infection coefficientspot blotch reaction type (0-9)spot blotch seedling infection response (1-9)spot blotch severityspot form net blotch (1-5)stem diameterstem lengthstem rust seedling reaction typestem rust severitystraw breakagestripe rust infection type (0-9)stripe rust severitytest weighttillers per plant T2tillers per plant T5total tocoltotal tocotrienolwinter hardinesswort colorwort protein

Analysis Method:

trial breeding program